Reading Microarray Data

Given an Agilent microarray, scanned intensity data converted with GenePix to *.gpr, I want to write automated R functions that will:
1. read only F532-BG column in each .gpr file in a directory
2. separate rows of data by block

chip1<-readGAL("08.23.2012_253295110035.gpr",path=NULL,header=TRUE,sep="\t",quote="\"",skip=NULL,as.is=TRUE)
> names(chip1)
 [1] "Block"                "Column"               "Row"                 
 [4] "Name"                 "ID"                   "X"                   
 [7] "Y"                    "Dia."                 "F532.Median"         
[10] "F532.Mean"            "F532.SD"              "F532.CV"             
[13] "B532"                 "B532.Median"          "B532.Mean"           
[16] "B532.SD"              "B532.CV"              "X....B532.1SD"       
[19] "X....B532.2SD"        "F532...Sat."          "F.Pixels"            
[22] "B.Pixels"             "Circularity"          "F532.Median...B532"  
[25] "F532.Mean...B532"     "F532.Total.Intensity" "SNR.532"             
[28] "Flags"                "Normalize"            "Autoflag"            
[31] "RefNumber"            "ControlType"          "GeneName"            
[34] "TopHit"               "Description" 
> good<-chip1$F532.Median...B532

References
[1] http://www.bioconductor.org/packages/2.12/bioc/vignettes/limma/inst/doc/usersguide.pdf

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About Lisa Cohen

PhD student at UC Davis.
This entry was posted in Bioconductor, limma, R. Bookmark the permalink.

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